def finish_initialization(experiment):
"""Finish an initialization"""
# Sharing is already started and the structures and energies have already
# been loaded into the Experiment
# Make the initial experiment summary
experiment["Summary"] = "Initial Calculations\n"
# Determine when they started
f = open(experiment["Folder"]+"initialize/Group1/Group1_Summary.txt","r")
for line in f:
if line.startswith("Started"):
experiment["Summary"] += line
break
f.close()
# Include the energies of each Design Group
for group in experiment:
experiment["Summary"] += SHARING.format_energies(\
experiment["Energies"][group.number], group.number, False)
# Create the initial folder in results
SHARING.output_best(experiment, 0, None)
# Figure out the name of the output file
if experiment["Type"] == "Mutator":
folder = experiment["Folder"] + "results/wildtype/"
else:
folder = experiment["Folder"] + "results/initial/"
# List the energies of each Target Molecule, too
if experiment["Energy Calculation"] == "Binding":
for molecule in experiment[0]:
if not molecule.design:
name = experiment["Folder"] + "initialize/Current/Molecule"
name += molecule.name + "_Energy.txt"
f = open(name, "r")
energy = f.readline().split()[2]
f.close()
experiment["Summary"] += "The energy of Target Molecule "
experiment["Summary"] += molecule.name + " is " + energy
experiment["Summary"] += " kcal / mol\n"
# Copy the file to the output folder
os.system("cp " + name + " " + folder)
# Move to the Experiment's folder
os.chdir(experiment["Folder"])
# Try to make the current folder
try:
os.mkdir("Current")
except OSError:
pass
# Write the Structures to the Current folder
SHARING.output_Current(experiment, "./Current/", None, 0)
experiment["Last Update"] = 0
# Start a refinment
REFINEMENT.Start(experiment, 0, None)
# Create the initial summary file
experiment["Summary"] += "Ended" + SHARING.time_stamp()
name = SHARING.summary_name(experiment["Folder"])
f = open(name, "w")
f.write(experiment["Summary"])
f.close()
# Remove the initialization folder
os.system("rm -rf initialize")
# End the sharing that was started elsewhere
SHARING.End(experiment)
def Calculate_Energy(experiment, gn = None):
"""Calculate the energies of an IPRO iteration"""
# Do the standard introductory checks
if not isinstance(experiment, EXPERIMENT.Experiment):
text = "The Calculate Energy function requires an Experiment class "
text += "object as its input."
raise IPRO_Error(text)
refinement = refinement_check(experiment, gn)
if refinement:
return {}, refinement
# Start timing
startTime = time.time()
# Store the energies here
energies = {}
# Loop through the Design Groups
for group in experiment:
if gn not in [None, group.number]:
continue
# Time the group
groupTime = time.time()
# initialize the dictionary
energies[group.number] = {}
# If there are no Target Molecules, it is impossible to calculate an
# interaction energy
do = False
for molecule in group:
if not molecule.design:
do = True
break
# Calculate the energies
if experiment["Force Field"] == "CHARMM":
complex = CHARMM.Energy(group, experiment, "all")
energies[group.number]["Complex"] = complex
if do:
design = CHARMM.Energy(group, experiment, True)
target = CHARMM.Energy(group, experiment, False)
energies[group.number]["Interaction"] = complex-design-target
else:
text = "The Calculate Energy function does not support the "
text += str(experiment["Force Field"]) + " force field."
raise IPRO_Error(text)
# update the summary
if gn == None:
experiment["Summary"] += SHARING.summary_update(groupTime, \
"Energy Calculation for Design Group " + str(group.number))
experiment["Summary"] +=SHARING.format_energies(energies[group.number],\
group.number, False)
experiment["Summary"] += SHARING.summary_update(startTime, \
"The Calculate Energy function")
return energies, refinement
def initialize_molecule(experiment, mn):
"""Initialize a Molecule"""
# Create the folder's name
folder = "Molecule" + mn
do = SHARING.claim_calculations(folder)
# If this processor is doing the calculations
if do:
# Make a summary
experiment["Summary"] = "Started" + SHARING.time_stamp()
# Move into the folder
os.chdir(folder)
SHARING.copy_standard_files(experiment)
# Get a unique copy of the Molecule
molecule = experiment[0][mn].duplicate()
for residue in molecule:
residue.freedom = "FREE"
# Store the calculated energies here
energies = {}
# Do a relaxation and energy calculation
if experiment["Force Field"] == "CHARMM":
CHARMM.Relaxation(molecule, experiment)
energies["Complex"] = CHARMM.Energy(molecule, experiment)
else:
text = "The initialize molecule function does not support the "
text += str(experiment["Force Field"]) + " force field."
raise IPRO_Error(text)
# Format the energy
text = SHARING.format_energies(energies)
experiment["Summary"] += text
# Create the summary file for the Molecule
experiment["Summary"] += "Ended" + SHARING.time_stamp()
name = SHARING.summary_name(SHARING.get_current())
f = open(name, "w")
f.write(experiment["Summary"])
f.close()
# Leave this folder, then start sharing
os.chdir('../')
SHARING.Start(experiment)
# Output the Molecule's structure
name = "./Current/" + molecule.generate_name()
molecule.output(name, molecule.fileFormat, experiment["User"])
# Output the Complex energy
f = open("./Current/Molecule" + mn + "_Energy.txt", "w")
f.write(text)
f.close()
# End sharing
SHARING.End(experiment)
def Finish(experiment, mn):
"""Finish the initial creation of a mutant"""
# Sharing was started in check finish
# Load the structures and energies
SHARING.update_Current(experiment, "./Current/")
SHARING.update_Energies(experiment, "./Current/")
# Create a brief summary of the information
experiment["Summary"] = '\nMutant ' + str(mn) + " Creation\n"
f = open("Group1/Group1_Summary.txt", "r")
for line in f:
if line.startswith("Started"):
experiment["Summary"] += line
break
f.close()
# Include information about the energies
for group in experiment:
experiment["Summary"] += \
SHARING.format_energies(experiment["Energies"][group.number], \
group.number, False)
# Put this in the overall summary
os.chdir(experiment["Folder"])
name = SHARING.summary_name(SHARING.get_current())
f = open(name, "a")
f.write(experiment["Summary"])
f.close()
# Make a folder to do the structure refinements in
folder = "mutant" + str(mn)
os.mkdir(folder)
folder += "/Current/"
os.mkdir(folder)
SHARING.output_Current(experiment, folder)
SHARING.output_Energies(experiment, folder)
f = open(folder + "iteration.txt", "w")
f.write(str(mn))
f.close()
# Delete the current folder
name = "initial_mutant" + str(mn)
os.system("rm -rf " + name)
# End sharing
SHARING.End(experiment)
def Finish(experiment, mn):
"""Finish the initial creation of a mutant"""
# Sharing was started in check finish
# Load the structures and energies
SHARING.update_Current(experiment, "./Current/")
SHARING.update_Energies(experiment, "./Current/")
# Create a brief summary of the information
experiment["Summary"] = '\nMutant ' + str(mn) + " Creation\n"
f = open("Group1/Group1_Summary.txt", "r")
for line in f:
if line.startswith("Started"):
experiment["Summary"] += line
break
f.close()
# Include information about the energies
for group in experiment:
experiment["Summary"] += \
SHARING.format_energies(experiment["Energies"][group.number], \
group.number, False)
# Put this in the overall summary
os.chdir(experiment["Folder"])
name = SHARING.summary_name(SHARING.get_current())
f = open(name, "a")
f.write(experiment["Summary"])
f.close()
# Make a folder to do the structure refinements in
folder = "mutant" + str(mn)
os.mkdir(folder)
folder += "/Current/"
os.mkdir(folder)
SHARING.output_Current(experiment, folder)
SHARING.output_Energies(experiment, folder)
f = open(folder + "iteration.txt", "w")
f.write(str(mn))
f.close()
# Delete the current folder
name = "initial_mutant" + str(mn)
os.system("rm -rf " + name)
# End sharing
SHARING.End(experiment)
def make_extra_group(experiment):
"""Create an extra Design Group with no Target Molecules"""
# Only do this if Binding energy calculations are being done
if experiment["Energy Calculation"] == "Binding":
# Get all of the Design Molecules from Design Group 1
molecules = []
for molecule in experiment[1]:
if molecule.design:
molecules.append(molecule)
# Make and store a new Design Group (which duplicates these Molecules
# for run independence reasons)
N = len(experiment) + 1
group = MOLECULES.DesignGroup(N, molecules, experiment["Force Field"], \
experiment["File Format"])
experiment._groupOrder.append(N)
experiment._groups[N] = group
n = len(experiment)
# Update the Current dictionary, too
experiment["Current"][n] = {}
for molecule in experiment[n]:
new = molecule.duplicate()
experiment["Current"][n][new.name] = new
# Those structures are essentially place holders at this point. However,
# we do need to run an energy minimization and calculate an initial
# energy for that group
name = "Group" + str(n) + "_Energies.txt"
SHARING.Start(experiment)
# If another processor already did the calculation, we're fine
if name not in os.listdir("./Current/"):
# Try to make a temp directory to do the calculations in
if "temp" not in os.listdir("./"):
# Make the directory and move into it
os.mkdir("temp")
os.chdir("temp")
# Stop sharing
SHARING.End(experiment)
# Copy in the relevant files
SHARING.copy_standard_files(experiment, False)
# Relax the Design Group
refinement = IPRO_FUNCTIONS.Relaxation(experiment, n, True)
# And calculate the energies
energies, refinement = \
IPRO_FUNCTIONS.Calculate_Energy(experiment, n)
# Move back up a folder
os.chdir("../")
# Start sharing
SHARING.Start(experiment)
# Store the energy
text = SHARING.format_energies(energies[n])
f = open("./Current/" + name, "w")
f.write(text)
f.close()
SHARING.output_Current(experiment, "./Current/", n)
# Delete the temp folder
os.system("rm -rf temp")
# Otherwise, just wait
else:
SHARING.End(experiment)
SHARING.Wait("temp", "./")
SHARING.Start(experiment)
# Store that complex energy
f = open("./Current/" + name, "r")
experiment["Energies"][n] = {"Complex": float(f.readline().split()[2])}
f.close()
SHARING.End(experiment)
def make_extra_group(experiment):
"""Create an extra Design Group with no Target Molecules"""
# Only do this if Binding energy calculations are being done
if experiment["Energy Calculation"] == "Binding":
# Get all of the Design Molecules from Design Group 1
molecules = []
for molecule in experiment[1]:
if molecule.design:
molecules.append(molecule)
# Make and store a new Design Group (which duplicates these Molecules
# for run independence reasons)
N = len(experiment) + 1
group = MOLECULES.DesignGroup(N, molecules, experiment["Force Field"], \
experiment["File Format"])
experiment._groupOrder.append(N)
experiment._groups[N] = group
n = len(experiment)
# Update the Current dictionary, too
experiment["Current"][n] = {}
for molecule in experiment[n]:
new = molecule.duplicate()
experiment["Current"][n][new.name] = new
# Those structures are essentially place holders at this point. However,
# we do need to run an energy minimization and calculate an initial
# energy for that group
name = "Group" + str(n) + "_Energies.txt"
SHARING.Start(experiment)
# If another processor already did the calculation, we're fine
if name not in os.listdir("./Current/"):
# Try to make a temp directory to do the calculations in
if "temp" not in os.listdir("./"):
# Make the directory and move into it
os.mkdir("temp")
os.chdir("temp")
# Stop sharing
SHARING.End(experiment)
# Copy in the relevant files
SHARING.copy_standard_files(experiment, False)
# Relax the Design Group
refinement = IPRO_FUNCTIONS.Relaxation(experiment, n, True)
# And calculate the energies
energies, refinement = \
IPRO_FUNCTIONS.Calculate_Energy(experiment, n)
# Move back up a folder
os.chdir("../")
# Start sharing
SHARING.Start(experiment)
# Store the energy
text = SHARING.format_energies(energies[n])
f = open("./Current/" + name, "w")
f.write(text)
f.close()
SHARING.output_Current(experiment, "./Current/", n)
# Delete the temp folder
os.system("rm -rf temp")
# Otherwise, just wait
else:
SHARING.End(experiment)
SHARING.Wait("temp", "./")
SHARING.Start(experiment)
# Store that complex energy
f = open("./Current/" + name, "r")
experiment["Energies"][n] = {"Complex":float(f.readline().split()[2])}
f.close()
SHARING.End(experiment)